They don't actually suggest downloading a gedcom, they suggest [at least that is what they did to me] downloading my ancestry tree INTO family tree maker [via family tree maker]. This will keep up with the member connections, people you've invited, etc. But lose the various FTM distinctives you mentioned.
So this works if your main tree is in ancestry and you just want to use FTM for backup. It does NOT work if FTM is your main tree and you want to keep its distinctives; in that case one needs to upload their FTM tree to ancestry, which then loses the people you've invited.
I decided long ago if my sync broke to stay with my FTM which is what I have now done. I'll just update ancestry tree by hand and concentrate on fixing my FTM tree so it shows sources better etc.
But the ancestry answer is so "cut and dried" as to "download your tree from ancestry" that they even gave me that answer when I was asking how to move to a new computer and keep the sync. Which is the WRONG answer for that.. thankfully I knew that much.